Ya, I'm not sure what to say. You and I have the exact same OS version and browser version... and I had very little trouble correcting the certificate issue. However, the one you are having trouble with is technically different. We've all been complaining about static.ak.facebook.com, and your link is for s-static.ak.facebook.com. -- Not that that should make a difference, the verification process should validate (or reject) all your certs.
S-static.ak.facebook.com is legit, but I can't tell if the s-static.ak.facebook.com certificate YOU have is malware without a screenshot of the details section expanded open (as its possible its a fake certificate).
I didn't try your re-direct link, but I did go to the NY Times website to see if I got the same issue, but I did not.
Also, as crampy said, I don't know why resetting Safari would have deleted your bookmarks etc... Now I feel bad for having suggested that (sorry). 😟